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Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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The Nucleosome Core Particle01:12

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Heterochromatin02:38

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
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H2A-H2B Histone Dimer Plasticity and Its Functional Implications.

Anastasiia S Kniazeva1, Grigoriy A Armeev1, Alexey K Shaytan1

  • 1Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.

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Summary

Histone H2A-H2B dimers stabilize nucleosomes and regulate DNA interactions. Their dynamics, influenced by DNA and histone sequences, are crucial for epigenetic regulation and nucleosome function.

Keywords:
H2A-H2B dimersMD simulationschromatinhistone variantshistonesmolecular modelingnucleosomenucleosome slidingstructural bioinformatics

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Structural Biology

Background:

  • Nucleosomes, the fundamental units of DNA packaging, consist of a histone octamer (H3-H4 tetramer and two H2A-H2B dimers).
  • H2A-H2B dimers are positioned at the nucleosome periphery, stabilizing the structure and modulating DNA dynamics like unwrapping and sliding.
  • Epigenetic regulation involves post-translational modifications and histone variants, but the direct link between H2A-H2B sequence, structure, and function is unclear.

Purpose of the Study:

  • To investigate the dynamics of histone H2A-H2B dimers in isolation and within nucleosomes.
  • To elucidate the relationship between H2A-H2B histone sequence, structure, dynamics, and nucleosome function.
  • To understand the mechanisms underlying nucleosome sliding, DNA unwrapping, and epigenetic modulation.

Main Methods:

  • Atomistic molecular dynamics simulations using Xenopus laevis histones.
  • Comparative analysis of structural data from databases.
  • Identification and characterization of major dynamical modes of H2A-H2B dimers.

Main Results:

  • A significant dynamical mode involving the bending of the longest H2A and H2B alpha-helices was identified.
  • The bending dynamics of H2A-H2B dimers are modulated by interactions with DNA, the H3-H4 tetramer, and DNA twist-defects.
  • The amino acid sequence of the histones plays a role in modulating these dynamics.

Conclusions:

  • The study provides detailed insights into the dynamics of H2A-H2B dimers, both free and in the context of nucleosomes.
  • These dynamics are influenced by multiple factors including DNA, other histones, and intrinsic sequence properties.
  • The findings illuminate the mechanisms governing nucleosome sliding, DNA unwrapping, and epigenetic modifications.